CHARLESTON, S.C., March 18 (Reuters) - A U.S. judge denied bond on Wednesday for an accused al Qaeda sleeper agent after prosecutors said he used his time in America to research information on toxins and was a colleague of suspected Sept. 11 mastermind Khalid Sheikh Mohammed.

Ali al-Marri, a 43-year-old with dual citizenship in Qatar and Saudi Arabia, was arrested in Illinois in December 2001 in an investigation of the Sept. 11 hijacked plane attacks.

Michael Mullaney, chief of the U.S. Justice Department's Counterterrorism Section, told the judge that Marri had entered the country on a student visa on Sept. 10, 2001, but never attended college classes, a violation of his visa.

Mullaney also said Marri failed to disclose on his application he had visited the United States in 2000 using a Saudi Arabian passport and had been arrested during a visit in the 1990s.

He did not elaborate on the arrest, but Marri's attorney said afterward it was for driving under the influence of alcohol. He said there was no information in the file on the disposition of that case.

"He was here at al Qaeda's request," the Justice Department official told the court. "While here, he continued to maintain contact with al Qaeda contacts back in Afghanistan."

The current indictment against Marri was void of detail and Mullaney did not elaborate on his assertion that Marri knew the accused al Qaeda operations leader, Mohammed, or that he studied toxins.

Marri was charged initially with credit card fraud and lying to the FBI, and pleaded not guilty. The charges were dropped in 2003 when then-President George W. Bush declared him an "enemy combatant" and sent him to the Consolidated Naval Brig in South Carolina. He was held in the military prison without charge and in extreme isolation for nearly six years.

Following a review ordered by President Barack Obama, Marri's case was transferred to the U.S. court system. A federal grand jury in Illinois indicted Marri last month on charges of conspiring with al Qaeda and providing material support for terrorism.

U.S. Magistrate Judge Robert Carr ordered U.S. marshals to take custody of Marri so he could be transferred to Illinois, where he is scheduled for arraignment on the charges on Monday in Peoria.

Assistant U.S. Attorney Kevin McDonald said after the hearing that Marri was a danger to the community and a flight risk but that he could offer no further information.

"I'll save the details for the trial team," he said.

Andrew Savage, Marri's attorney, criticized prosecutors for not sharing any of their evidence against his client. "If he is who they say he is, why can't we evaluate it?" he said.

NO THREAT TO AMERICAN VALUES

Savage said afterward the decision to deny bail for Marri was not a surprise, but "I stand by my statement that he is not in any way shape or form a threat to America or American values."

He argued in the bond hearing his client had been a model prisoner. He called as witnesses the brig's senior civilian leader and a military policeman who often guarded Marri, both of whom testified that Marri followed brig regulations and never tried to escape or espoused anti-American views.

Savage's wife and legal assistant, Cheryl Savage, described her contacts with Marri over the years.

"He is very devout. His religion is very important to him," she said. "It is the essence of who he is."

Cheryl Savage described a trip she and her husband made to visit Marri's family in Qatar and Saudi Arabia, and her husband showed the court video clips of Marri's brothers and children, whom he had not seen in more than seven years.

Cheryl Savage offered to put up her family's commercial real estate as collateral if Marri was granted bond. The law firm's private investigator, a former FBI agent with 30 years of experience, said he had prepared a security plan to ensure the community's safety if Marri was released.

The judge said that illustrated why Marri should not be released. (Editing by Jane Sutton; Editing by Peter Cooney)